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\bibitem{de2002comparative}
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\newblock Comparative analysis of chloroplast genomes: functional annotation,
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\newblock Complete chloroplast genome sequence of holoparasite cistanche
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\bibitem{guindon2005phyml}
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\newblock Phyml online—a web server for fast maximum likelihood-based
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\bibitem{mcfadden2001primary}
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\newblock Primary and secondary endosymbiosis and the origin of plastids.
\newblock {\em Journal of Phycology}, 37(6):951--959, 2001.

\bibitem{parra2000geneid}
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\bibitem{parra2007cegma}
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\newblock {\em Bioinformatics}, 23(9):1061--1067, 2007.

\bibitem{Rice2000}
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\bibitem{RDOGMA}
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\newblock Automatic annotation of organellar genomes with dogma.
\newblock {\em BIOINFORMATICS, oxford Press}, 20(172004):3252--3255, 2004.

\bibitem{stamatakis2008raxml}
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\newblock {\em Department of Computer Science.
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\bibitem{stamatakis2005raxml}
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\newblock {\em Bioinformatics}, 21(4):456--463, 2005.

\bibitem{sugawara2008ddbj}
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